Contacts of the helix formed by residues 377 - 388 (chain D) in PDB entry 1KU7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 377 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375D LYS 4.2 0.2 + - - -
376D LEU* 1.3 76.2 - - - +
378D GLU* 1.3 66.1 + - - +
379D ARG* 3.7 7.1 + - - +
380D GLU* 2.7 42.5 + - - +
381D ALA* 3.0 21.4 + - - +
422D LYS* 4.7 2.0 - - - +
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Residues in contact with GLU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A SER* 2.8 31.1 + - - +
367A GLU* 5.8 3.2 - - - +
370A GLU* 4.3 8.2 - - - +
376D LEU 4.1 0.2 + - - -
377D SER* 1.3 73.2 - - - +
379D ARG* 1.3 60.3 + - + +
381D ALA* 3.5 5.4 + - - +
382D MET* 3.0 30.5 + - - +
385D LYS* 5.7 1.8 + - - -
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Residues in contact with ARG 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D SER* 3.2 6.3 + - - +
378D GLU* 1.3 80.8 - - + +
380D GLU* 1.3 60.3 + - + +
382D MET* 3.6 4.6 - - - +
383D VAL* 2.8 38.1 + - - +
405D PHE* 3.5 46.8 + - + +
407D VAL* 4.2 19.5 - - - +
411D ARG* 3.9 17.2 - - - +
415D ILE* 3.6 34.9 - - - +
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Residues in contact with GLU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D LEU* 3.2 11.9 - - + +
377D SER* 2.7 46.7 + - - +
379D ARG* 1.3 77.8 - - + +
381D ALA* 1.3 63.6 + - - +
383D VAL* 3.2 3.3 + - - +
384D LEU* 3.1 26.6 + - - +
415D ILE* 4.3 23.3 - - + +
418D LYS* 4.4 14.9 - - - +
419D ALA* 3.9 18.9 + - + -
422D LYS* 2.9 39.9 + - - +
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Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 5.0 0.3 - - - +
376D LEU* 4.5 20.5 - - + +
377D SER 3.0 15.4 + - - +
378D GLU* 3.8 5.2 - - - +
380D GLU* 1.3 77.0 - - - +
382D MET* 1.3 56.7 + - - +
384D LEU* 3.2 7.6 + - - +
385D LYS* 2.9 52.5 + - - +
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Residues in contact with MET 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A SER 4.2 18.4 - - - +
369A LEU* 3.7 29.2 - - + -
370A GLU* 4.5 9.2 - - - +
378D GLU* 3.0 26.6 + - - +
379D ARG* 3.6 5.8 - - - +
381D ALA* 1.3 74.5 - - - +
383D VAL* 1.3 66.7 + - - +
385D LYS* 4.3 5.8 - - - +
386D MET* 2.9 55.6 + - + +
391D ILE* 3.8 25.1 - - + -
404D TYR* 4.0 10.3 - - + +
405D PHE* 3.8 22.2 - - + -
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Residues in contact with VAL 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D ARG* 2.8 34.0 + - + +
380D GLU 3.4 5.8 - - - +
382D MET* 1.3 71.5 - - - +
384D LEU* 1.3 59.1 + - + +
386D MET* 3.9 1.2 - - - +
387D ARG* 3.0 34.4 + - + +
401D VAL* 4.6 6.2 - - + +
405D PHE* 3.7 26.0 - - + -
412D ILE* 4.1 27.6 - - + +
415D ILE* 3.9 18.6 - - + -
416D GLU* 4.1 28.3 - - + +
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Residues in contact with LEU 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 3.5 26.7 - - + -
376D LEU* 4.4 8.3 - - + -
380D GLU 3.1 10.5 + - - +
381D ALA* 3.4 10.3 - - - +
382D MET 3.1 0.2 - - - -
383D VAL* 1.3 80.2 - - + +
385D LYS* 1.3 61.9 + - - +
387D ARG* 3.4 3.0 + - - +
388D LYS* 3.0 33.6 + - - +
416D GLU* 3.9 31.0 - - + +
419D ALA* 3.8 30.1 - - + -
420D LEU* 4.3 11.4 - - + -
423D LEU* 3.6 31.0 - - + -
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Residues in contact with LYS 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A GLU* 2.8 44.3 + - - +
373A LEU* 4.2 9.4 - - + -
385A LYS* 5.4 12.1 - - - +
390A LEU* 4.0 17.5 - - + -
378D GLU* 5.7 2.0 + - - -
381D ALA* 2.9 42.1 + - - +
382D MET* 3.8 6.7 - - - +
384D LEU* 1.3 73.3 - - - +
386D MET* 1.3 60.9 + - - +
389D GLY 3.3 1.6 + - - -
390D LEU* 2.8 43.9 + - + -
391D ILE* 3.4 18.0 + - + -
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Residues in contact with MET 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LEU* 3.7 17.7 - - + -
433A LEU* 3.9 23.3 - - + -
382D MET* 2.9 49.9 + - + +
383D VAL* 3.9 3.1 - - - +
385D LYS* 1.3 78.7 - - - +
387D ARG* 1.3 62.1 + - - +
389D GLY* 3.6 6.1 + - - -
391D ILE* 3.9 11.6 - - + +
392D ASP* 5.2 0.2 - - - +
394D ARG 3.7 0.3 - - - +
396D HIS* 3.3 43.0 + - + -
400D GLU 5.4 0.4 - - - +
401D VAL* 4.2 25.1 - - + -
404D TYR* 3.9 32.8 - - + -
405D PHE* 5.0 1.3 - - - -
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Residues in contact with ARG 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D VAL* 3.0 27.4 + - + +
384D LEU* 3.9 2.9 - - - +
386D MET* 1.3 76.4 - - - +
388D LYS* 1.3 65.0 + - + +
389D GLY 3.2 0.4 - - - -
395D GLU* 3.3 27.5 - - - +
396D HIS* 2.8 33.3 + - - +
397D THR* 3.6 4.9 - - - +
398D LEU* 3.4 37.7 - - - +
401D VAL* 3.9 19.1 - - + -
412D ILE* 4.7 1.1 - - + -
416D GLU* 2.7 45.4 + - - +
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Residues in contact with LYS 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LYS* 3.6 63.4 + - + +
390A LEU* 3.9 19.1 - - + -
395A GLU* 5.5 6.5 + - - +
384D LEU* 3.0 24.3 + - - +
387D ARG* 1.3 81.6 - - - +
389D GLY* 1.3 59.2 + - - +
390D LEU* 3.5 9.5 + - + +
395D GLU* 4.2 10.9 - - - +
416D GLU* 3.2 26.1 + - - -
420D LEU* 5.1 15.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il